MHD Simulations of Core Collapse Supernovae with Cosmos++

We performed 2D, axisymmetric, MHD simulations with Cosmos++ in order to examine the growth of the magnetorotational instability (MRI) in core--collapse supernovae. We have initialized a non--rotating 15 solar mass progenitor, infused with differential rotation and poloidal magnetic fields. The collapse of the iron core is simulated with the Shen EOS, and the parametric Ye and entropy evolution. The wavelength of the unstable mode in the post--collapse environment is expected to be only ~ 200 m. In order to achieve the fine spatial resolution requirement, we employed remapping technique after the iron core has collapsed and bounced. The MRI unstable region appears near the equator and angular momentum and entropy are transported outward. Higher resolution remap run display more vigorous overturns and stronger transport of angular momentum and entropy. Our results are in agreement with the earlier work by Akiyama et al. (2003) and Obergaulinger et al. (2009).Comment: 3 pages, 2 figures. To appear in the proceedings of the "Deciphering the Ancient Universe with Gamma-Ray Bursts", April 2010, Kyoto, Japan, eds. N. Kawai and S. Nagataki (AIP

The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA-DNA hybrids.

Telomerase is an enzyme that adds repetitive DNA sequences to the ends of chromosomes and consists of two main subunits: the telomerase reverse transcriptase (TERT) protein and an associated telomerase RNA (TER). The telomerase essential N-terminal (TEN) domain is a conserved region of TERT proposed to mediate DNA substrate interactions. Here, we have employed single molecule telomerase binding assays to investigate the function of the TEN domain. Our results reveal telomeric DNA substrates bound to telomerase exhibit a dynamic equilibrium between two states: a docked conformation and an alternative conformation. The relative stabilities of the docked and alternative states correlate with the number of basepairs that can be formed between the DNA substrate and the RNA template, with more basepairing favoring the docked state. The docked state is further buttressed by the TEN domain and mutations within the TEN domain substantially alter the DNA substrate structural equilibrium. We propose a model in which the TEN domain stabilizes short RNA-DNA duplexes in the active site of the enzyme, promoting the docked state to augment telomerase processivity

Discretized rotation has infinitely many periodic orbits

For a fixed k in (-2,2), the discretized rotation on Z^2 is defined by (x,y)->(y,-[x+ky]). We prove that this dynamics has infinitely many periodic orbits.Comment: Revised after referee reports, and added a quantitative statemen

Structural basis of template-boundary definition in Tetrahymena telomerase.

Telomerase is required to maintain repetitive G-rich telomeric DNA sequences at chromosome ends. To do so, the telomerase reverse transcriptase (TERT) subunit reiteratively uses a small region of the integral telomerase RNA (TER) as a template. An essential feature of telomerase catalysis is the strict definition of the template boundary to determine the precise TER nucleotides to be reverse transcribed by TERT. We report the 3-Å crystal structure of the Tetrahymena TERT RNA-binding domain (tTRBD) bound to the template boundary element (TBE) of TER. tTRBD is wedged into the base of the TBE RNA stem-loop, and each of the flanking RNA strands wraps around opposite sides of the protein domain. The structure illustrates how the tTRBD establishes the template boundary by positioning the TBE at the correct distance from the TERT active site to prohibit copying of nontemplate nucleotides

Dynamical Imaging with Interferometry

By linking widely separated radio dishes, the technique of very long baseline interferometry (VLBI) can greatly enhance angular resolution in radio astronomy. However, at any given moment, a VLBI array only sparsely samples the information necessary to form an image. Conventional imaging techniques partially overcome this limitation by making the assumption that the observed cosmic source structure does not evolve over the duration of an observation, which enables VLBI networks to accumulate information as the Earth rotates and changes the projected array geometry. Although this assumption is appropriate for nearly all VLBI, it is almost certainly violated for submillimeter observations of the Galactic Center supermassive black hole, Sagittarius A* (Sgr A*), which has a gravitational timescale of only ~20 seconds and exhibits intra-hour variability. To address this challenge, we develop several techniques to reconstruct dynamical images ("movies") from interferometric data. Our techniques are applicable to both single-epoch and multi-epoch variability studies, and they are suitable for exploring many different physical processes including flaring regions, stable images with small time-dependent perturbations, steady accretion dynamics, or kinematics of relativistic jets. Moreover, dynamical imaging can be used to estimate time-averaged images from time-variable data, eliminating many spurious image artifacts that arise when using standard imaging methods. We demonstrate the effectiveness of our techniques using synthetic observations of simulated black hole systems and 7mm Very Long Baseline Array observations of M87, and we show that dynamical imaging is feasible for Event Horizon Telescope observations of Sgr A*.Comment: 16 Pages, 12 Figures, Accepted for publication in Ap

The aggregation of cytochrome C may be linked to its flexibility during refolding

Large-scale expression of biopharmaceutical proteins in cellular hosts results in production of large insoluble mass aggregates. In order to generate functional product, these aggregates require further processing through refolding with denaturant, a process in itself that can result in aggregation. Using a model folding protein, cytochrome C, we show how an increase in final denaturant concentration decreases the propensity of the protein to aggregate during refolding. Using polarised fluorescence anisotropy, we show how reduced levels of aggregation can be achieved by increasing the period of time the protein remains flexible during refolding, mediated through dilution ratios. This highlights the relationship between the flexibility of a protein and its propensity to aggregate. We attribute this behaviour to the preferential urea-residue interaction, over self-association between molecules

Similar dissection of sets

In 1994, Martin Gardner stated a set of questions concerning the dissection of a square or an equilateral triangle in three similar parts. Meanwhile, Gardner's questions have been generalized and some of them are already solved. In the present paper, we solve more of his questions and treat them in a much more general context. Let $D\subset \mathbb{R}^d$ be a given set and let $f_1,...,f_k$ be injective continuous mappings. Does there exist a set $X$ such that $D = X \cup f_1(X) \cup ... \cup f_k(X)$ is satisfied with a non-overlapping union? We prove that such a set $X$ exists for certain choices of $D$ and $\{f_1,...,f_k\}$. The solutions $X$ often turn out to be attractors of iterated function systems with condensation in the sense of Barnsley. Coming back to Gardner's setting, we use our theory to prove that an equilateral triangle can be dissected in three similar copies whose areas have ratio $1:1:a$ for $a \ge (3+\sqrt{5})/2$

Radiative Lifetimes of Single Excitons in Semiconductor Quantum Dots- Manifestation of the Spatial Coherence Effect

Using time correlated single photon counting combined with temperature dependent diffraction limited confocal photoluminescence spectroscopy we accurately determine, for the first time, the intrinsic radiative lifetime of single excitons confined within semiconductor quantum dots. Their lifetime is one (two) orders of magnitude longer than the intrinsic radiative lifetime of single excitons confined in semiconductor quantum wires (wells) of comparable confining dimensions. We quantitatively explain this long radiative time in terms of the reduced spatial coherence between the confined exciton dipole moment and the radiation electromagnetic field.Comment: 4 pages, 3 figure

Optical Identification of the ASCA Large Sky Survey

We present results of optical identification of the X-ray sources detected in the ASCA Large Sky Survey. Optical spectroscopic observations were done for 34 X-ray sources which were detected with the SIS in the 2-7 keV band above 3.5 sigma. The sources are identified with 30 AGNs, 2 clusters of galaxies, and 1 galactic star. Only 1 source is still unidentified. The flux limit of the sample corresponds to 1 x 10^{-13} erg s^{-1} cm^{-2} in the 2-10 keV band. Based on the sample, the paper discusses optical and X-ray spectral properties of the AGNs, contribution of the sources to the Cosmic X-ray Background, and redshift and luminosity distributions of the AGNs. An interesting result is that the redshift distribution of the AGNs suggests a deficiency of high-redshift (0.5 10^{44} erg s^{-1}) absorbed narrow-line AGNs (so called type 2 QSOs).Comment: Accepted for publication in ApJ. 57 pages with 13 figures, 9 JPG plates, 5 additional PS tables. Original EPS plates (gzipped format ~1Mbyte/plate) and TeX tables are available from ftp://ftp.kusastro.kyoto-u.ac.jp/pub/akiyama/0001289